Those planning to leave London Euston after 8pm are set to be hardest hit with three services already cancelled.
The staff shortages, blamed on "short-term operational issues" are said to specifically affect trains between MK and London but will lead to Northampton services being busier with some passengers being forced on to rail replacement buses.
A London Northwestern statement issued just after 1pm said: " On Sunday evening (June 20) we are likely to have to cancel or make changes to a number of our trains to and from London Euston, due to a shortage of available train crew.
"We are advising you to check your journey using our journey planner, and consider travelling earlier than you may have originally planned.
"It may not be possible to maintain social distancing on some of our trains this evening.
"We will arrange for rail replacement bus services to help fill the gaps in our train service, where we are able.
"We're really sorry for the inconvenience this may cause you. This is due to short-term operational issues."